Understanding global patterns of biodiversity change is crucial for conservation research, policies and practices. However, the lack of systematically collected data at a global level has limited our understanding of biodiversity changes and their local-scale drivers in most ecosystems. We address this challenge by focusing on wetlands, which are among the most biodiverse and productive environments providing essential ecosystem services, but are also amongst the most seriously threatened ecosystems. Using birds as an indicator taxon of wetland biodiversity, we model time-series abundance data for 461 waterbird species at 25,769 survey sites across the globe. We show that countries’ effective governance is the strongest predictor of waterbird abundance changes as well as benefits of conservation efforts. Waterbirds are declining especially where governance is, on average, less effective, such as Western/Central Asia, sub-Saharan Africa and South America. Higher protected area coverage facilitates waterbird increases, but only in countries with more effective governance. Our findings highlight that sociopolitical instability can lead to biodiversity loss and also undermine the benefit of existing conservation efforts, such as the expansion of protected area coverage. Data deficiency in areas with less effective governance could cause an underestimation of the extent of biodiversity crisis. Alternative language abstracts are in Supplementary Information.